NCBI Database on Cycloartenol Synthase

Mohammad Basyuni1,2, Rahmah Hayati1, Yuntha Bimantara1, Rizka Amelia1, Sumaiyah3, Era Yusraini4, and Hirosuke Oku5 1Department of Forestry, Faculty of Forestry, Universitas Sumatera Utara, Jl. Tri Dharma Ujung No. 1 Medan, North Sumatera 20155, Indonesia 2Mangrove and Bio-Resources Group, Center of Excellence for Natural Resources Based Technology, Universitas Sumatera Utara, Medan North Sumatera 20155, Indonesia. 3Faculty of Pharmacy, Universitas Sumatera Utara, Medan 20155, Indonesia 4Faculty of Agriculture, Universitas Sumatera Utara, Medan 20155, Indonesia 3Molecular Biotechnology Group, Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan

Keywords: Abiotic stress, cycloartenol, isoprenoid, oxidosqualene

Abstract: Cycloartenol synthase (EC 5.4.99.8) is a cycloartenol-converting enzyme. The current research describes the search of cycloartenol synthase databases from the National Center for Biotechnology Information (NCBI). A amount of precious information was generated by NCBI database search (https:/www.ncbi.nlm.nih.gov/). Results discovered in 22 cycloartenol synthase databases. All literature, genes, genetics, protein, genomes, and chemical features of cycloartenol synthase databases. Bookshelf, MeSH (Medical Subject Headings) and PubMed Central were discussed in the literature. Gene was made up of profiles from Gene, Gene Expression Omnibus (GEO), HomoloGene, PopSet, and UniGene. Data on genetics such as MedGen was available for cycloartenol synthase. Proteins characteristic comprised Conserved Domains, Identical groups of proteins, clusters of proteins, sparcle, and structure. Nucleotide and sample were engaged in genomes. BioSystems, PubChem BioAssay, PubChem Compound, and PubChem Substance are the chemical properties. The present work affords vital information in term biotechnology of cycloartenol synthase.

1 INTRODUCTION are accountable for biosynthesis of phytosterol, and more OSCs are committed for triterpene Phytosterol including cycloartenol is ordinary synthesis (Thimmappa et al., 2014). chemical constituents in higher plants (Augustin et Lanosterol and cycloartenol are significant al., 2011; Uddin et al., 2015). Phytosterols serve as elements of the membrane and can provide chemotaxonomy markers also have been shown substrates for hormones of sterols (Bloch 1983). (Koch et al., 2011). Many phylogenetic analyses Our previous studies have shown that membrane have been suggested that plant oxidosqualene lipids (triterpenoids and phytosterols) have an cyclases (OSCs) are generally evolutionarily evident role in mangrove modification to salinity derived from cycloartenol synthase (Zhang et al., stress (Oku et al., 2003; Basyuni et al., 2009, 2003; Basyuni et al., 2007a,b). More than 2012a,b), Saccharomyces cerevisiae, GIL77, thousands different OSC genes together with modulated the salt tolerance of lanosterol synthase cycloartenol have been reported from plant deficient (Inafuku et al., 2018). Even though a kingdom, which are expanded from a shared 2,3- significant number of studies in cycloartenol oxidosqualene substrate via OSCs, they separate in synthases have been well documented (Agustin et the cyclization of this intermediacy into each of al., 2011; Xue et al., 2012; Gas-Pascual et al., phytosterol of cycloartenol and lanosterol or a 2014; Moses et al., 2014; Thimmappa et al., 2014;), diversity of triterpenes (Augustin et al., 2011). In Limited work concentrated on biotechnology data plantae, cycloartenol synthase (CAS) along with from all accessible databases in cycloartenol lanosterol synthase (LAS), family member of OSC synthases. Here we report an alternative technique

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Basyuni, M., Hayati, R., Bimantara, Y., Amelia, R., Sumaiyah, S., Yusraini, E. and Oku, H. NCBI Database on Cycloartenol Synthase. DOI: 10.5220/0008386800160019 In Proceedings of the International Conference on Natural Resources and Technology (ICONART 2019), pages 16-19 ISBN: 978-989-758-404-6 Copyright c 2019 by SCITEPRESS – Science and Technology Publications, Lda. All rights reserved

NCBI Database on Cycloartenol Synthase

to collect useful data needed in latest Furthermore, 87 Pubmed and 232 PubMed Central biotechnology-related science studies on documentations were stored as called the plant cycloartenol synthase through a preferred search cycloartenol synthase (Table 1). The PubMed engine. Therefore, the aim of this research was to database includes quotes derived different topics in explain the implementation of the National Center many connections to reports of full-text papers on for Biotechnology Information (NCBI) databases rubber plants open access. (GQuery) search to gain more deepful information on updated cycloartenol synthesis biotechnology. Table 2: Genes source NCBI database for cycloartenol synthase Health Amount Explanation 2 MATERIALS AND METHODE Gene 242 Gathered data about the gene loci GEO Profiles 116 Gene profile and molecular The search engine for NCBI databases abundance patterns (https:/www.ncbi.nlm.nih.gov/) was used to HomoloGene 2 Homologous gene sets for produce a amount of useful rubber plant data chosen organisms biotechnology. As stated previously on September PopSet 3 Sets of phylogenetic and population studies sequences 19, 2018, data bases were obtained by writing UniGene 66 Groups of transcripts Hevea brasiliensis in all database searches. All conveyed databases composed of literature, health, genes, protein, genomes, and chemical properties were Table 3: Genetics source NCBI database for cycloartenol featured. Cycloartenol synthase (GQuery) was synthase performed. The bookshelf, MeSH (Medical Genetics Total Information Subject Headings), NLM (National Medicine MedGen 1 Literature and connections in Library) Catalog, PubMed, PubMed Central, EST, medical genetics Gene, GEO datasets, PopSet, Identical Protein Groups, Protein, Sparde, Structure, Assembly, Table 4: Proteins source NCBI database for cycloartenol BioProject, BioSample, Genome, GSS, Nucleotide, synthase Probe, SRA, Taxonomy, Biosystems, and Proteins Number Explanation PubChem BioAssay were the data variables. Conserved 1 Preserved protein domains Domains Identical 723 Sequences of proteins Protein classified by similarity 3 RESULTS AND DISCUSSIONS Groups Protein 976 Sequences of proteins Table 1 demonstrates the literature on cycloartenol Protein 17 Sequence of protein clusters synthase available in the NCBI. Four biographies Clusters based on similarity Structure 2 Experimentally determined stored in countless numbers. The web NCBI biomolecular structures literature provides internet libraries and free access to bookshelf data (two reports and books), 2 MeSH Table 5: Genomes source NCBI database for Plant and (Medical Subject Headings), namely cycloartenol cycloartenol synthase synthase [Supplementary Concept] and 3-beta-(2- (diethylamino) ethoxy) androst-5-en-17-one [ Genomes Number Description Nucleotide 1583 RNA and DNA sequences Additional Concept], ontology used to index PubMed papers. Probe 92 Biomolecular structures experimentally determined Table 1: Literature source NCBI database for cycloartenol synthase Information on genes sources is displayed in Literature Total Information Table 2. This data is as well as genes associated to Bookshelf 2 Reports and books cycloartenol synthase than consisting of 242 genes Mesh 2 Medical topic in the with top organisms are Rosa chinensis (15), Malus collections of the NLM domestica (14), Camellia sinensis (11), Zea mays PubMed 312 Scientific and medical (10), Pyrus x bretschneideri (10), Gossypium abstracts/quotations PubMed 584 Articles in full-text journals hirsutum (10), G. raimondii (10), Vitis vinifera Central (10), Aegilops tauschii (8), Arachis hypogaea (8),

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Brachypodium distachyon (7), Phoenix dactylifera Biosystems, 107 PubChem bioassay, 22 PubChem (7), Nicotiana tabacum (7), and all other taxa. compound, and 58 PubChem substance. Table 2 shows there is 116 GEO profiles, one homologene, three popset, and 66 uniges. It is Table 6: Chemicals source NCBI database for important to note that top organisms for unigene cycloartenol synthase are Malus domestica (5), Zea mays (5), Panicum Chemicals Total Information virgatum (4), Brassica napus (3), Arabidopsis BioSystems 10234 Molecular pathways thaliana (3), Citrus sinensis (3), Medicago associated to genes, proteins truncatula (3), Vitis vinifera (3), Triticum aestivum and chemicals (3), and Pinus taeda (3). The three popsets are PubChem 107 Bioactivity screening Nicotiana tabacum cycloartenol synthase (CAS1) BioAssay PubChem 22 Chemical data with systems, mRNA, complete cds, Bacillariophyta cycloartenol Compound experience and relationships synthase gene, partial cds, and Avena cycloartenol synthase gene, complete cds. PubChem 58 Substance stored and Table 3 shows one genetics information on Substance chemical data medical genetics literature and links. On the other hand, Table 4 depicts protein source from NCBI Protein modeling of cycloartenol synthase from database for there are five sources for protein that mangrove trees has recently been defined (Basyuni consists of one conserved domain, 723 identical et al. 2018). The protein modeling for KcCAS in protein groups, 976 proteins, 17 protein clusters, Kandelia candel and RsCAS of Rhizophora stylosa and two structures. The conserved domains cycloartenol synthases was analyzed by Pyre2 comprise C-terminal domain of squalene-hopene showed homolous results with lightly divergent in cyclase. EC:5.4.99.17 registered as squalene- sequence similarity. By disparity, the Swiss model hopene cyclase, in bacteria activates the cyclisation for KcCAS had marginally greater sequence of squalene into hopene. This response is partly homology (47.3%) and differentiated Qmean cationic cyclisation cascade, to be similar to a (0.70) from RsCAS. critical level in cholesterol biosynthesis. The C- terminal half of the molecule belongs to this family (Marchler-Bauer et al., 2016). 4 CONCLUSIONS The same protein groups combined from 13 invertebrates, 437 plants and fungi, and 26 The web NCBI defines multiple biological and prokaryotes. It is interesting to note that 976 biotechnology data on cycloartenol synthase. The proteins are consisting of animals (2), plants (797), current work motivated scientists in the field of fungi (1), protists (85), bacteria (90) and archaea biotechnology to obtain more advantages using the (1). Top organism for plants are 51 Oryza sativa NCBI search engine. The present study also (International Rice Genome Sequencing Project, delivers crucial data regarding biotechnology of 2005), 46 Vitis vinifera (Roach et al., 2018) and triterpene synthases. 46 Zea mays (Soderlund et al., 2009), 21 Medicago truncatula (Young et al., 2011), and 20 Arabidopsis thaliana (Corey et al., 1993). The two structures of cycloartenol are structure ACKNOWLEDGMENTS of human OSC in complex with Ro 48-8071 [Isomerase, EC: 5.4.99.7] and Human OSC This work was in part assisted by an International structure in lanosterol complex [Isomerase, EC: Research Collaboration and Scientific Publication 5.4.99.7]. Grant 2019 from Universitas Sumatera Utara. Table 5 displays 1583 nucleotides that comprising of Animals(6), Plants(1,294), Fungi(1), Protists(111), Bacteria(171), Archaea(1). The top REFERENCES plant species as following Oryza sativa (55), Malus domestica (45), Zea mays (43), Glycine Augustin, J.M., Kuzina, V., Andersen, S.B. and Bak, S., max (27), Vitis vinifera (27), and all other taxa 2011. Molecular activities, biosynthesis and (1097). There are 92 probes in the cycloartenol evolution of triterpenoid saponins. Phytochemistry, synthase. Table 6 describes the chemical source of 72, 435-457. the NCBI database that consists of 10234 Basyuni, M., Oku, H., Tsujimoto, E., Kinjo, K., Baba, S. and Takara, K., 2007a. Triterpene synthases from the

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Okinawan mangrove tribe, Rhizophoraceae. The Moses, T., Papadopoulou, K.K. and Osbourn, A., 2014. FEBS Journal, 274(19), 5028-5042. Metabolic and functional diversity of saponins, Basyuni, M., Oku, H., Tsujimoto, E., and Baba, S. 2007b. biosynthetic intermediates and semi-synthetic Cloning and functional expression of cycloartenol derivatives. Critical reviews in biochemistry and synthases from mangrove species Rhizophora molecular biology, 49(6), pp.439-462. stylosa Griff. and Kandelia candel (L.) Druce. Roach, M. J., Johnson, D. L., Bohlmann, J., et al., 2018. Bioscience, Biotechnology, and Biochemistry, 71(7), Population sequencing reveals clonal diversity and 1788-1792. ancestral inbreeding in the grapevine cultivar Basyuni, M., Baba, S., Inafuku, M., Iwasaki, H., Kinjo, Chardonnay. PLoS Genetics, 14(11), e1007807. K. and Oku, H., 2009. Expression of terpenoid Soderlund, C., Descour, A., Kudrna, D., et al., 2009. synthase mRNA and terpenoid content in salt Sequencing, mapping, and analysis of 27,455 maize stressed mangrove. Journal of Plant Physiology, full-length cDNAs. PLoS Genetics, 5(11), e1000740. 166(16), 1786-1800. Thimmappa, R., Geisler, K., Louveau, T., O'Maille, P. Basyuni, M., Baba, S., Kinjo, Y., Putri, L.A., Hakim, L. and Osbourn, A., 2014. Triterpene biosynthesis in and Oku, H., 2012a. Salt-dependent increase in plants. Annual Review of Plant Biology, 65, pp.225- triterpenoids is reversible upon transfer to fresh 257. water in mangrove plants Kandelia candel and Uddin, M. S., Sarker, M. Z. I., Ferdosh, S., Akanda, M. J. Bruguiera gymnorrhiza. Journal of Plant H., Easmin, M. S., Bt Shamsudin, S. H., & Yunus, K. Physiology, 169(18), 1903-1908. B. (2015). Phytosterols and their extraction from Basyuni, M., Baba, S., Kinjo, Y., and Oku, H. 2012b. various plant matrices using supercritical carbon Salinity increases the triterpenoid content of a salt dioxide: a review. Journal of the Science of Food secretor and a non-salt secretor mangrove. Aquatic and Agriculture, 95(7), 1385-1394. Botany, 97(1), 17-23. Xue, Z., Duan, L., Liu, D., et al., 2012. Divergent Basyuni, M., Sulistiyono, N., Wati, R., Oku, H., Baba, S., evolution of oxidosqualene cyclases in plants. New and Sagami, H. 2018. Predicted cycloartenol Phytologist, 193(4), 1022-1038. synthase protein from Kandelia obovata and Young, N. D., Debellé, F., Oldroyd, G. E., et al., 2011. Rhizophora stylosa using online software of Phyre2 The Medicago genome provides insight into the and Swiss-model. Journal of Physics : Conference evolution of rhizobial symbioses. Nature, 480(7378), Series, 978 (1), 012077. 520. Bloch, K. E. 1983. Sterol, structure and membrane function. Critical Reviews in Biochemistry, 14(1), 47-92. Corey, E. J., Matsuda, S. P., and Bartel, B. 1993. Isolation of an Arabidopsis thaliana gene encoding cycloartenol synthase by functional expression in a yeast mutant lacking lanosterol synthase by the use of a chromatographic screen. In Proceedings of the National Academy of Sciences, 90(24), 11628-11632. Gas-Pascual, E., Berna, A., Bach, T. J., and Schaller, H. 2014. Plant oxidosqualene metabolism: cycloartenol synthase–dependent sterol biosynthesis in Nicotiana benthamiana. PLoS One, 9(10), e109156. Inafuku, M., Basyuni, M., and Oku, H. 2018. Triterpenoid modulates the salt tolerance of lanosterol synthase deficient Saccharomyces cerevisiae, GIL77. Saudi Journal of Biological Sciences, 25(1), 1-9. International Rice Genome Sequencing Project 2005. The map-based sequence of the rice genome. Nature, 436(7052), 793. Koch, B. P., Souza Filho, P. W., Behling, H., et al., 2011. Triterpenols in mangrove sediments as a proxy for organic matter derived from the red mangrove (Rhizophora mangle). Organic Geochemistry, 42(1), 62-73. Marchler-Bauer, A., Bo, Y., Han, L., et al., 2016. CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic acids research, 45(D1), D200-D203.

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